ArticlePLoS genetics2011
A population genetics-phylogenetics approach to inferring natural selection in coding sequences.
Article in PLoS genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed, 89 citations in OpenAlex.
- Epistasis among clustered lineage-specific amino acid substitutions in the Drosophila Trio protein.PLoS genetics · 2026Article
- Epistasis among clustered lineage-specific adaptive amino acid substitutions in the Drosophila Trio protein.bioRxiv : the preprint server for biology · 2025Article
- Positive selection at core genes may underlie niche adaptation in Fusobacterium animalis.Gut pathogens · 2025Article
- Online toolkits for collaborative and inclusive global research in urban evolutionary ecology.Ecology and evolution · 2024Article
- Selective events at individual sites underlie the evolution of monkeypox virus clades.Virus evolution · 2023Article
- Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales.Virus evolution · 2022Article
- Inferring Long-Term Effective Population Size with Mutation-Selection Models.Molecular biology and evolution · 2021Article
- Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2.Genome biology and evolution · 2021Article
- Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond.Journal of molecular evolution · 2021Article
- Mutation rates and selection on synonymous mutations in SARS-CoV-2.bioRxiv : the preprint server for biology · 2021Article
- Adaptation of the endemic coronaviruses HCoV-OC43 and HCoV-229E to the human host.Virus evolution · 2021Article
- GenomegaMap: Within-Species Genome-Wide dN/dS Estimation from over 10,000 Genomes.Molecular biology and evolution · 2020Article
- Computational Inference of Selection Underlying the Evolution of the Novel Coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2.Journal of virology · 2020Article
- Past and ongoing adaptation of human cytomegalovirus to its host.PLoS pathogens · 2020Article
- Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species.Molecular biology and evolution · 2020Article
- Intrinsically disordered regions are abundant in simplexvirus proteomes and display signatures of positive selection.Virus evolution · 2020Article
- Detecting adaptive convergent amino acid evolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Review
- Genetic conflicts with Plasmodium parasites and functional constraints shape the evolution of erythrocyte cytoskeletal proteins.Scientific reports · 2018Article
- Exonic splice regulation imposes strong selection at synonymous sites.Genome research · 2018Article
- Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
Through an analysis of polymorphism within and divergence between species, we can hope to learn about the distribution of selective effects of mutations in the genome, changes in the fitness landscape that occur over time, and the location of sites involved in key adaptations that distinguish modern-day species. We introduce a novel method for the analysis of variation in selection pressures within and between species, spatially along the genome and temporally between lineages. We model codon evolution explicitly using a joint population genetics-phylogenetics approach that we developed for the construction of multiallelic models with mutation, selection, and drift. Our approach has the advantage of performing direct inference on coding sequences, inferring ancestral states probabilistically, utilizing allele frequency information, and generalizing to multiple species. We use a Bayesian sliding window model for intragenic variation in selection coefficients that efficiently combines information across sites and captures spatial clustering within the genome. To demonstrate the utility of the method, we infer selective pressures acting in Drosophila melanogaster and D. simulans from polymorphism and divergence data for 100 X-linked coding regions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.